Abstract: Types and quantities of microorganisms vary with time in the process of fermentation of Kombucha,leading to difficult to control the metabolites.The high-throughput sequencing technology was used to study the 7th day of traditional Kombucha.And the total of 65771178 clean reads was obtained,which produced 93449 Unigene by assembling. These Unigene were annotated using BLAST(E-value<1.0e^-5)against the NR,KEGG database. A total of 65515 Unigenes were compared with the NR Library for comment information,and then according to the relationship between GI(GenInfo Identifier)and species classification to obtain the gene set of species classification information. It was found that traditional Kombucha were divided into two kingdoms including bacteria and fungi. Bacteria made up for 96.57%,fungi only accounted for 3.40%. Gluconacetobacter sp. SXCC-1(29.17%),Komagataeibacter medellinensis(7.84%)and Komagataeibacter xylinus(7.58%)were identified as the dominant bacterium in Kombucha samples.At the same time,Brettanomyces bruxellensis(1.86%)was identified as the dominant fungi. The KEGG database as a reference 47234 Unigenes in the metagenomic could be divided into 338 classes metabolic pathway. Of these,2475 Unigene were found to be related to amino acid metabolism,and 307 were involved in secondary metabolic biosynthesis. This metagenomic raw data was deposited in GenBank under the accession SRP103682.The traditional Kombucha microorganism was identified to the "species" level by metagenomic technology,while understanding the metabolic mechanism of Kombucha microbial fermentation process,and the process of fermentation of Kombucha can be more effectively controlled.